Extended Data Fig. 1: Visualization of transcriptome deconvolution into 2 gene modules.

a, Application of surprisal analysis to the RNA-seq data atlases related to T cell exhaustion. Samples from two representative T cell exhaustion studies (GSE89307 and GSE86881) were shown antigen-specific CD8⁺ T cells from acute Listeria infection and tumour progression (right), and from chronic LCMV infection (left). In the acute/tumour model, TCR-transgenic naïve T cells were transferred prior to pathogen or tumour induction, with effector/memory and early/late exhausted states sampled across defined time points. In the chronic model, naïve and late exhausted T cells were isolated from spleens following persistent LCMV infection. The combination of the gene expression baseline and the first two gene modules accurately recapitulated the experimentally measured transcriptome profiles. Heatmaps display genes positively or negatively associated with Module 1 or Module 2 (red = high, blue = low). Sample annotations follow standard naming conventions. b,c, GSEA enrichment of pathways based on genes positively or negatively associated in Module 1 (M1, b) and Module 2 (M2, c). GSEA uses a one-sided, permutation-based modified K–S test with adjustments for multiple comparisons. d,e, Module scores for M1 and M2 were calculated using a time-series T cell RNA-seq dataset of acute and chronic LCMV infection (GSE41867) (d, n = 4 independent samples), and projected onto a two-dimensional map with the x- and y-axes representing the respective module scores (e). f, Heat map showing expression of E3-related genes in adoptively transferred T cells from spleen, and in double negative (DN, PD-1⁻TIM-3⁻), single positive (SP, PD-1⁺TIM-3⁻), and double positive (DP, PD-1⁺TIM-3⁺) cells from B16-OVA tumours at day 14 after ACT (n = 3 independent samples). g, Percentages for E3 ligase-related genes predicted to be correlated (orange) or anti-correlated (blue) with exhaustion are shown. h, Volcano plot showing differential expression of E3-related genes between PD-1⁻TIM-3⁻ and PD-1⁺TIM-3⁺ TILs. The x-axis represents the log₂transformed fold change (FC) values, and the y-axis represents the negative log₁₀ of adjusted P values (n = 3 independent samples). i, GSEA of ubiquitin-associated pathways in 400,000 human TILs with functional versus dysfunctional mitochondria (defined by the activity of mitochondrial complex I) across 21 cancer types. j, GSEA of ubiquitin-associated pathways in tumour-specific TILs with (MTDR/MTG)^hi versus (MTDR/MTG)^lo mitochondria from a mouse ACT model. k,l, Venn diagrams showing 78 E3 ligase genes negatively linked to T cell exhaustion, identified by overlapping differentially expressed genes from two gene modules (M1 and M2) with a curated E3 ligase list (k), and 133 E3 ligase genes positively associated with mitochondrial function, shared between mouse and human T cells (l).